Table 1 Average AUC values for simulation data with replicates

PG1

33 %

50 %

50 %

60 %

60 %

70 %

80 %

PG2

33 %

30 %

40 %

20 %

30 %

20 %

10 %

PG3

33 %

20 %

10 %

20 %

10 %

10 %

10 %

(a) P_DEG = 5 %

EEE-E (TCC)

91.57

91.50

91.50

91.43

91.42

91.45

91.46

DDD-D (TCC)

90.70

90.62

90.64

90.54

90.55

90.59

90.62

SSS-S (TCC)

88.34

88.33

88.30

88.24

88.23

88.21

88.30

E-E (edgeR)

91.58

91.48

91.47

91.38

91.37

91.38

91.34

edgeR_robust

90.95

90.86

90.85

90.75

90.74

90.74

90.73

D-D (DESeq)

90.71

90.60

90.60

90.50

90.49

90.50

90.48

S-S (DESeq2)

88.34

88.31

88.26

88.19

88.17

88.11

88.14

voom

87.16

87.01

86.99

86.88

86.91

86.88

86.86

SAMseq

85.04

84.97

84.93

84.83

84.88

84.88

84.91

PoissonSeq

87.31

87.25

87.25

87.19

87.17

87.22

87.23

baySeq

90.24

90.21

90.21

90.22

90.17

90.13

90.07

EBSeq

85.77

85.85

85.78

85.81

85.73

85.71

85.77

(b) P_DEG = 25 %

EEE-E (TCC)

91.47

91.46

91.45

91.45

91.43

91.42

91.37

DDD-D (TCC)

90.77

90.73

90.72

90.70

90.68

90.65

90.57

SSS-S (TCC)

88.13

88.11

88.13

88.14

88.12

88.09

88.06

E-E (edgeR)

91.47

91.30

91.18

91.06

90.98

90.62

89.97

edgeR_robust

90.89

90.69

90.57

90.43

90.34

89.97

89.27

D-D (DESeq)

90.77

90.54

90.37

90.25

90.15

89.73

89.04

S-S (DESeq2)

88.12

87.83

87.62

87.49

87.36

86.79

85.92

voom

87.08

86.71

86.52

86.29

86.18

85.60

84.56

SAMseq

84.95

84.82

84.82

84.77

84.75

84.72

84.63

PoissonSeq

87.22

87.18

87.14

87.13

87.11

87.06

86.97

baySeq

90.34

90.13

90.07

89.92

89.83

89.52

88.86

EBSeq

85.82

85.61

85.49

85.34

85.30

84.74

84.02